Madin–Darby canine kidney cells are increased in aerobic glycolysis when cultured on flat and stiff collagen‐coated surfaces rather than in physiological 3‐D cultures

We investigate the influence of the dimensionality and the biochemistry of the culture system on the cellular functionality by analyzing the protein expression levels in Madin–Darby canine kidney (MDCK) cells grown in 3‐D and 2‐D substrates. We cultured MDCK cells on a hard and flat 2‐D uncoated plastic surface, on a 2‐D collagen‐coated plastic surface and in 3‐D collagen gel and employed 2‐D gel electrophoresis, MALDI‐TOF‐MS, and LC‐MS/MS analysis to identify the differentially regulated proteins. We found significant differences in the expression of antioxidant proteins, actin‐binding proteins, glycolytic enzymes, and heat‐shock proteins/chaperons among the three types of cultures. While MDCK cells cultured in 3‐D collagen up‐regulate antioxidant proteins and proteins involved in the dynamic remodeling of the actin cytoskeleton, 2‐D collagen‐coated plastic surfaces induce the up‐regulation of glycolytic enzymes. Our data shows that the culture conditions have profound effects on the physiology of the cell. Culture in 3‐D collagen induces a differentiated polarized phenotype. In contrast, collagen‐coated 2‐D substrates favor a tumor‐like phenotype with increased glycolysis. Thus, the suitability of 2‐D cultures to study the physiological behavior of cells, especially in drug discovery, bioprocessing, and toxicology, should be carefully reconsidered.     

Follow the leader: preference for specific amino acids directly following the initial methionine in proteins of different organisms

It is well established that the vast majority of proteins of all taxonomical groups and species are initiated by an AUG codon, translated into the amino acid methionine (Met). Many attempts were made to evaluate the importance of the sequences surrounding the initiation codon, mostly focusing on the RNA sequence. However, the role and importance of the amino acids following the initiating Met residue were rarely investigated, mostly in bacteria and fungi. Herein, we computationally examined the protein sequences of all major taxonomical groups represented in the Swiss-Prot database, and evaluated the preference of each group to specific amino acids at the positions directly following the initial Met. The results indicate that there is a species-specific preference for the second amino acid of the majority of protein sequences. Interestingly, the preference for a certain amino acid at the second position changes throughout evolution from lysine in prokaryotes, through serine in lower eukaryotes, to alanine in higher plants and animals.     

基于Petri网T不变量的PHB新陈代谢建模分析(英文)

从拓扑结构的角度分析生化反应网络是生物信息学研究中的一个热点问题。通过将两种传统的途径分析方法(基元模式和极端途径)与Petri网的T不变量分析进行了比较,结果表明:它们本质上是一致的,但是采用Petri网的T不变量分析更便捷。然后,利用Petri网技术构建了PHB代谢模型。对该模型作了结构分析,将计算得到的23个T不变量进行了分组:I组表示简单的可逆反应,II组表示循环的反应,III组可用于调控ATP/ADP比率,IV组是与PHB生产直接相关的反应,可用于代谢工程以提高PHB的产率。最后讨论了Petri网的T不变量分析在这个领域中的应用。     

Effects of land use on aquatic macrophyte diversity and water quality of ponds

1. Aquatic macrophyte diversity and water quality of 55 ponds in western Japan were related to land use and morphometric variables to identify the environmental factors that sustain biodiversity and the spatial extent at which these factors operate. 2. The relevant spatial extent for floating‐leaved macrophyte richness (500 m from pond edge) was larger than that for submerged macrophyte occurrence (10, 75 and 100 m), whereas emergent macrophyte richness was best explained at much larger extents (1000 m). Total macrophyte richness was explained at the extent of 500, 750 and 1000 m. The extents relevant for explaining the physicochemical condition of pond water (100 and 250 m) were similar to those for submerged and floating‐leaved macrophytes, suggesting that these two growth forms are more sensitive to water quality compared to emergent macrophytes. 3. Diversity of all three growth forms and that of total macrophytes collectively were inversely related to turbidity and nutrient concentration; among the three growth forms, submerged macrophytes were most affected by water quality. 4. Negative relationships were found between the proportion of urban area and the diversity of the three growth forms and that of total macrophytes and water quality. Species richness of emergent, floating‐leaved and total macrophytes decreased with depth and increased with surface area up to about 5000 m², above which it declined. 5. Urbanisation and enlargement of ponds were the two main factors that decreased aquatic macrophyte diversity in irrigation ponds. To alleviate the adverse effects of urban areas on aquatic macrophyte diversity, our results suggest that management efforts should focus on the creation of buffer zones within the relevant spatial extent from the pond edge.     

Deep intra-uterine artificial inseminations using cryopreserved spermatozoa in beluga (Delphinapterus leucas)

Artificial insemination (AI) with liquid-stored spermatozoa and sperm cryopreservation using directional freezing (DF) have been successful in the beluga. This study built on this foundation to develop a deep intra-uterine AI technique with frozen-thawed semen in beluga. Forty-two ejaculates from one male were cryopreserved using DF technology and subsequently used for 10 insemination attempts with seven females. Percentage pre- and post-thaw progressive motility and viability were (mean ± SD) 73.0 ± 12.2, 38.4 ± 8.8, 88.0 ± 0.1, and 59.3 ± 15.7%, respectively. A series of GnRH injections (3 x 250 μg, IV, 1.5 to 2 h apart) were used to induce ovulation, once a growing follicle >2.5 cm in diameter was visualized via trans-abdominal ultrasonography. Artificial insemination was performed at 30.1 ± 3.8 h post-initial GnRH injection with semen deposited in the uterine horn, 92.6 ± 16.2 cm beyond the genital opening using a flexible endoscope. The external cervical os (cEOS) was located beyond a series of 5 to 10 vaginal rings, 44.8 ± 9.3 cm from the external genital opening. The internal bifurcation of the uterus was 27 ± 6.8 cm beyond the cEOS. Ovulation occurred at 8.5 ± 7.6 h post-AI. Two of 10 inseminations (20%) resulted in pregnancy. The first pregnancy resulted in twins; both calves were born 442 d after AI, with one surviving. The second pregnancy is ongoing. These findings represent the first successful application of AI using frozen-thawed semen in beluga, and are important examples of how assisted reproductive technologies can provide tools for the global management of threatened species.     

Aspects of community ecology of amphibians and reptiles at Bonny Island (Nigeria), an area of priority relevance for petrochemical industry

Finima Nature Park, situated in Bonny Island (Niger Delta, Nigeria), is a protected forested area placed within one of the most industrially developed (and environmentally polluted) regions of the whole African continent. Amphibian and reptile community composition in relation to season and microhabitat characteristics was studied, by a combination of field techniques, during the wet and dry seasons of 2007 and 2008. Overall, a total of 21 species of reptiles from nine families (with 668 individuals caught) and eight amphibian species from five families (492 individuals caught) were recorded. Nearly 94% of the amphibian individuals and most of the species were recorded, especially during the wet season, whereas most of the reptiles were found with no inter‐seasonal differences. However, Agama agama and Mabuya affinis were found especially during the dry season. As for microhabitat use, the reptile species showed a clear, aggregated preference for two microhabitat types (dry leaves and under logs), which are probably crucial when these animals need to lose body temperature to avoid overheating. Concerning amphibians, the various species used the available microhabitats in a way expectable from their main ecological traits, with toads differing from aquatic frogs, and these differing from arboreal frogs.     

Biology of the solitary wasp Trypoxylon (Trypargilum) agamemnon Richards 1934 (Hymenoptera: Crabronidae) in trap‐nests

Buschini, M.L.T. and Fajardo, S. 2009. Biology of the solitary wasp Trypoxylon (Trypargilum) agamemnon Richards 1934 (Hymenoptera: Crabronidae) in trap‐nests. —Acta Zoologica (Stockholm) 91 : 426–432. Some Trypoxylon species build their nests in preexisting tubular cavities like hollow stems and beetle borings in branches. Study of the biology of these insects is relatively easy because the females of these wasps nest with enormous success in trap‐nests. The aim of this study was to investigate the abundance, seasonality and life‐history of Trypoxylon agamemnon. For capture of these insects, trap‐nests were installed in the Parque Municipal das Araucárias in araucaria forest, grassland and swamp, from December, 2001 to December, 2005. Two hundred and ninety seven nests were obtained. They were constructed more often during the summer (from December to April). The nests were built only in araucaria forest and consisted of a linear series of cells, divided by mud partitions, whose number varied from 1 to 7. Normally they have only one vestibular cell. The inner cells had been provisioned, usually with spiders of Anyphaenidae family. Sex‐ratio was strongly female biased. Its main natural enemies included Chrysididae, Ichneumonidae and Tachinidae.     

A prime inference on genetic diversity (RAPDs) in the marine fish Atherinella brasiliensis (Teleostei,Atherinopsidae) from Southern Brazil

Da Silva Cortinhas, M. C., Glienke, C., Prioli, A. J., Noleto, R. B., Matoso, D. A. and Cestari, M. M. 2010. A prime inference on genetic diversity (RAPDs) in the marine fish Atherinella brasiliensis (Teleostei, Atherinopsidae) from Southern Brazil. —Acta Zoologica (Stockholm) 91 : 242–248 As a result of the importance of Atherinella brasiliensis in estuarine environments, random amplified polymorphic DNA (RAPD) markers were used to verify the genetic diversity in A. brasiliensis from two different places in Paranaguá Bay (Paraná State) and one from the Conceição Lagoon (Santa Catarina State). Cytogenetic data have shown a high karyotypic diversity in some populations, although in others this peculiarity demonstrates rearrangements such as heterochromatinization. In the present study, a low level of genetic structuring between the samples from Conceição Lagoon compared with the others was observed through principal coordinate analysis (PCO), analysis of molecular variance and Mantel test according to 79 RAPD markers. As this specie does not perform horizontal migration and the individuals of Conceição Lagoon are isolated, three hypotheses are proposed to explain the results: (i) similar environments may show homogeneous populations not depending on the geographical distance, (ii) because vicariant events that formed the bays occurred in a recent period, the fragmentation effects over the structuring of the genetic diversity may still be low and not totally detectable by the RAPD technique and (iii) the isolation time or the number of generations may not be enough to promote a possible differentiation and genetic structuring between the specimens of these three places. The specimens of these places present a low level of differentiation and genetic structuring so we can consider them as a unique homogeneous population.     

Gene expression changes in spleens of the wildlife reservoir species, Eurasian wild boar （Sus scrofa）, naturally infected with Brucella suis biovar 2

Brucella suis is responsible for swine brucellosis worldwide.Of the five different 8.suis biovars (bv.), bv.2 appears restricted to Europe where it is frequently isolated from wild boar and hares, can infect pigs and can cause human brucellosis.In this study, the differ-ential gene expression profile was characterized in spleens of Eurasian wild boar naturally infected with B.suis by.2.Of the 20,201 genes analyzed in the microarray, 633 and 1,373 were significantly (fold change＞1.8; P＜0.01) upregulated and downregulated, respectively,in infected wild boar.The analysis was focused on genes that were over represented after conditional test for biological process gene on-tology.Upregulated genes suggested that B.suis bv.2 infection induced cell maturation, migration and/or proliferation in infected animals.The genes downregulated in infected wild boar impaired the activity of several important cellular metabolic pathways such as metabolism,cytoskeleton organization and biogenesis, immune response and lysosomal function and vesicle-mediated transport.In addition, the re-sponse to stress, sperm fertility, muscle development and apoptosis seemed to be also impaired in infected animals.These results sug-gested that B.suis by.2 may use strategies similar to other smooth brucellae to facilitate intraeellular multiplication and the developmentof chronic infections.To our knowledge, this is the first report of the analysis of gene expression profile in hosts infected with B.suis by.2, which is important to understand the molecular mechanisms at the host-pathogen interface in the main reservoir species with possible implications in the zoonotic cycle of the pathogen.